Sonic: Trainer Adventure
by Lunala - get in the bag
Summary: It seemed like a normal adventure. Grab the 7 Chaos Emeralds, go Super, defeat Eggman, save the day. Unfortunately, Sonic could only find 6 out of the 7 emeralds. When Sonic thought he defeated Eggman, he tries to send Sonic and his friends to a different world, but something went wrong. Sonic's gonna need new friends to save this new world. (DISCONTINUED)
1. Prologue

**Edit 1: Changed some speech.  
Edit 2: Added more dialogue and Shadow.**

"Speech"  
" _Pokemon Speech_ "  
 _Thoughts  
_ _Pokemon Move_

* * *

"Looks like I've beat you once again, Egghead! I'm amazed you still try after all these years." Sonic smirked.

"Hmmph." Shadow grunted. "Just another victory." _But why do I feel like something is wrong?_ He thought. But Eggman had a desperate Plan B up his sleeve. Ignoring Sonic's comment, he pressed a wireless button.

"Sonic!" Sonic's friends shouted. Sonic, who thought that he defeated Eggman, fell for his trap. A hole opened up in the wall, and launched a strong metal hand at Sonic. The Blue Blur did not expect this, and was punched to the side. His 6 Chaos Emeralds clattered as they hit the ground. More holes opened up, and grabbed Sonic, Tails and Knuckles, immobilizing them.

Shadow dodged the claw, however. He tried to grab the emeralds, but more claws shot out. Knocking out two with a strong kick and one with a punch, a claw grabbed him from behind.

Sonic the Hedgehog, the world-wide hero that never gives up, has failed. In his most vulnerable moment, Dr. Eggman captured the heroes by surprise. With the 6 Chaos Emeralds out of Sonic's possession, Eggman put them into a machine with the other 7th. This machine would finally get rid of Sonic, once and for all. It would send him into a completely different world. However, this machine would not be strong enough alone. It needed the power of all 7 Chaos Emeralds.

"Muahahahaha! Sometimes, the simplest answer is the best answer!" Eggman laughed maniacally. As he held down the button, the machine rumbled to life, and a large laser cannon started to glow, pointing right at the group of four. "Goodbye, Sonic! FIRE!"

However, there was a large flash. Not from the cannon itself, but from two mysterious figures. The flash died down, to reveal a certain hedgehog and cat. The hedgehog thew up a shield, and the laser hit the shield, and a bright flash occured. If somebody else was there, they would notice that the room was empty.

* * *

Waves were splashing, birds were singing, and a small breeze was blowing. Sonic, who just opened his eyes, knew something was different. For one, there was waves, birds, and a breeze. He definitely wasn't on a flowery field next to a beach a few seconds ago, and there wasn't an unfamiliar voice trying to talk to him. Oh, he should probably listen.

 _"Oh! You're awake!"_ Said a small feminine voice. Sonic looked down, and saw a small white hedgehog-like creature with a grass-like back. She had pink flowers next to her ears. "My name is Shaymin. Who might you be? I don't think I've seen a Pokemon like you before."

"Oh, hello Shaymin. My name's Sonic. But I have a question. What's a Pokemon?"

 _"You... don't know what a Pokemon is?"_ Shaymin asked, puzzled by the question. " _You're not from around here, aren't you?_ "

"No." Sonic replied.

 _"Ah, that would explain it."_ Suddenly, there was rustling from a nearby bush. Another strange creature appeared, which might be one of those Pokemon Shaymin was talking about. It was roughly half the size of Sonic, and was seemingly levitating. It had a short red lower body, with big wings, even though they weren't flapping. It's upper body was white, and on top of the long neck was a small head with amber eyes. It had a blue triangle on it's chest. " _Oh hi Latias! Come meet my new friend!_ " Shaymin greeted. _"Latias, meet Sonic."_

 _"Well, hi Sonic! I've never seen a Pokemon like you."_ Sonic sweat-dropped, having to go through this again.

 _"I don't think he is a Pokemon!"_ Shaymin explained bluntly. Latias raised an eyebrow.

 _"But- what?"_

"Well, I guess I should explain..."

* * *

"Hey Latias, what is that blue orb thing? I sense somebody's soul inside of it." Sonic asked. Turns out that Sonic landed in a hidden grotto nearby a city called Altomare. Latias said that they couldn't go to Altomare itself, however. They would think Sonic was a new Pokemon, and be captured. Speaking of which, Sonic didn't want to test if he could be captured.

" _That is the soul dew. It keeps the water clean, as well as calm it down when something disturbs it. However, it has a flaw. It needs the power of a legendary Pokemon's soul for it to work._ "

"Oh. Well, who's soul is in there?"

" _...My brother's..._ " Latias said gloomily after a moment.

"Oh, I'm sorry. I didn't know..."

" _It's okay. It's been a while since that happened, and I've gotten over it._ " An awkward silence passed by.

Sonic then had an idea. "Say... I have a question. Is your brother dead, or just trapped inside there?"

" _I... don't actually know. All I know is that there doesn't seem to be a way to revive him..._ "

* * *

"That's troubling..." Said Bianca.

The only people that know about Sonic's story is Shaymin (who lost her way and ended nearby Latias's home three years after the events of Pokemon Heroes), Latias, and their friends Bianca and Lorenzo. "Indeed," said the old man. "these jewels could be anywhere! And if somebody evil stumbles across something with that much power..."

"Needless to say, it wouldn't be pleasant." finished Sonic (who found out he can understand both Pokemon and Human speech).

Lorenzo sighed. "Then I guess there is only one thing to do. Sonic, this looks like the start of a new journey. You'll have to travel across the world and find these emeralds fast and first."

"I've got it covered, Lorenzo. Besides, I've done it before, I can certainly do it again!" Sonic smirked, slowly standing up from the chair, making sure he didn't drop Shaymin.

" _I-I want to help!_ " Said the Gratitude Pokemon.

"What? Really?"

" _I want to help too._ " The Eon Dragoness smiled. " _You've got friends. And a good friend helps a friend in need._ " Latias telepathed, which the humans could hear (after months of training).

But Bianca looked confused. "But Latias, you're not much of a fighter."

" _I always wanted to be a medic._ "

"Well I guess the matter's settled. We've got a long trip ahead of us, so we should get a good night's sleep." Everybody agreed with Lorenzo, and went to bed (or in Sonic and Shaymin's case, couch).

* * *

 **The next morning...**

* * *

"I'm gonna miss you, Latias." Bianca cried.

" _Don't be sad. When days go by and I'm still out there, be happy, knowing that I'm gonna help save the world._ " Latias smiled, and went in for a "goodbye" hug.

"Be safe out there, you three." Said the old man. Shaymin plucked a gracidea flower out from the ground and put it in Sonic's new travel bag. "Speaking of safe, I want you protected from other trainers. So here are some Pokeballs." Lorenzo put the 6 balls in Sonic's hand. "These balls are made for capturing and storing Pokemon, sort of like a whole dimension that can fit in your pocket for the Pokemon stored inside. I suggest that you use your first two on Latias and Shaymin."

 _Wow, and I thought that Tails' inventions were cool. This is awesome!_ "You ready girls?" Sonic asked. The two nodded, and Sonic tossed 2 balls. They didn't even shake before the balls clicked, signifying the capture was a success.

"In case you find any more Pokemon, here is a Pokedex. It will scan any known Pokemon, and it will tell you information about it." Lorenzo handed over the Pokedex, which was surprisingly thin, after Sonic put the balls in the bag.

"Wait, Sonic, how will you be getting across this sea?" Bianca asked.

"Well, let's just say they call me the fastest thing alive for a reason! See ya guys later!" Sonic turned to the water, and _boosted_ across the water.

* * *

 **And that's the prologue done! Tell me how you guys think of this story so far. And just keep in mind that the "chapters" I post are really just rough drafts. I do this so that if I write down something that I'm not too fond of, you can let me know what you think of it. If you don't like it either, then I can change it.**

 _ **Sonic's Team:**_

 _ **Shaymin  
Latias**_


	2. Chapter 1: A Wild Pokemon Appears!

**Edit 1: Fixed some mistakes, and added a bit more dialogue.**

"Speech"  
" _Pokemon Speech_ "  
 _Thoughts_  
 _Pokemon Move_

* * *

 **Previously...**

* * *

 _"Looks like I've beat you once again, Egghead! I'm amazed you still try after all these years."_

 _"Muahahahaha! Sometimes, the simplest answer is the best answer!"_

"My name is Shaymin. Who might you be? I don't think I've seen a Pokemon like you before."

"Latias, meet Sonic."

"Well, hi Sonic! I've never seen a Pokemon like you."

 _"That's troubling..." Said Bianca._

 _"_ I want to help too. _" The Eon Dragoness smiled. "_ You've got friends. And a good friend helps a friend in need. _"_

 _"_ I always wanted to be a medic. _"_

 _"I'm gonna miss you, Latias." Bianca cried._

 _"You ready girls?" Sonic asked. The two nodded, and Sonic tossed 2 balls. They didn't even shake before the balls clicked, signifying the capture was a success._

 _"Well, let's just say they call me the fastest thing alive for a reason! See ya guys later!" Sonic turned to the water, and_ boosted _across the water._

* * *

 **Chapter 1: A Wild Pokemon Appeared!**

* * *

Land finally came into view, and Sonic took a pit stop there. "Land ho!" Sonic called, releasing Shaymin and Latias. They both blinked. " _Already? That was like, two minutes!_ " Latias was surprised.

"Well back on my world, I'm known as the fastest thing alive." Sonic smirked, wagging a finger.

" _Geez, you'll give the fastest Pokemon a run for their money._ " Latias rolled her eyes. They noticed Shaymin in her Sky forme come flying over.

" _I found a village nearby. I think it's called New Bark Town. Seems like a quiet place. How about we head there?_ "

"Well sure!" Sonic was about to start walking, when he remembered to put them in their balls. However, Latias dodged the beam.

" _I can turn invisible, so I can stay out of the ball._ "

"Oh, cool!"

* * *

 **Music: Route 29 - Pokemon Heart Gold & Soul Silver**

* * *

"We probably shouldn't head into town, so let's head down this path." It smelled like freshly cut grass.

It seemed to be a long path, so Sonic simply jogged, and let Shaymin ride his shoulder. After a while, they came across a sign. **"Left - Cherrygrove City | New Bark Town - Right | Route 46 - Up"**

However, it seemed Route 46 was inaccessible at the time, so they went to Cherrygrove. On the way, they came across a tree full of berries. "Well don't mind if I do." Sonic commented, setting Shaymin down.

" _What are you doing-_ " " _Sonic wait-_ " Shaymin and Latias got caught off when Sonic started to roll into a ball, and spin in place. After a few seconds, Sonic went blasting off, and _spindashed_ into the tree, knocking out all the berries. Unfortunately, there were some wild Pokemon in the tree.

" _Sonic!_ " Latias scolded as the Pidgey fell out. He merely let out an oops. Shaymin dug into the bag sitting on the ground, and pulled out the Pokedex.

" **Pidgey: The Tiny Bird Pokemon. Pidgey is a Flying Pokémon. Among all the Flying Pokémon, it is the gentlest and easiest to capture. A perfect target for the beginning Pokémon Trainer to test his Pokémon's skills. Pidgey's Gust power creates tornadoes. It also has a Sand-Attack."**

Because of all the noise the fallen Pidgey's created, a bigger not-Pidgey, for lack of better words, came flying over and tried to do a _quick attack._ Sonic dodged out of the way.

 **"Pidgeotto: The Bird Pokemon. Pidgeotto is the evolved form of the Pidgey. It is armed with sharp claws and dives from the sky to capture its prey. Unlike the more gentle Pidgey, Pidgeotto can be dangerous. Approach with extreme caution."**

 **Music: Wild Pokemon! (Johto) - Pokemon Anime**

" _You! I may not know what you are, but you are trespassing my territory! I will finally prove myself to my family!_ " She squawked.

"You looking for a fight, eh?" Sonic replied.

" _I've got this one!_ " Shaymin flew over.

"Ready, Shaymin? Use _Magical Leaf_!" Nearby leaves gained a magical glow, and started to float around. Turning sharp, they flew fast towards Pidgeotto. However, she blocked with her wings, dealing less damage. She then flapped her wings quite hard, causing a strong _gust_. Shaymin was blown back, and Sonic quickly yelled, "Counter with a _quick attack!"_ Pidgeotto was sent flying back, hitting the ground hard. Seeing a chance, Shaymin threw a final set of _Magical Leaves_ at the bird, defeating her.

 **Music: Victory! Wild Pokemon - Pokemon Omega Ruby & Alpha Sapphire**

"Nice job, Shaymin!" Sonic cheered. Shaymin _tackled_ Sonic affectionately, even if it didn't do a thing due to how light she was. " _Good job!_ " Latias echoed. Sonic pet Shaymin as she dropped her flight.

" _I am a disgrace to my flock..._ " Pidgeotto sobbed. Sonic noticed that the Pidgeotto was crying, and kneeled down next to her. In the moment, he forgot about Shaymin and she dropped to the ground.

"Hey, don't cry. You just need to practice more." Sonic encouraged.

" _That's not it... M-My family treats me like trash... I ch-challenged you so I-I could prove myself I wasn't th-the things they called me..._ " She paused to take a breath. " _But y-you defeated me, and now I only proved I am trash..._ "

"No, you're not trash. Nobody is trash. You just haven't been able to unlock your full potential. Say, if you come with me, I can make you stronger."

" _R-Really?_ " She asked, blinking away tears.

"Yeah. If you accept, just press this button." Sonic pulled out a spare Pokeball and held it above her head. She thought about it for a full 30 seconds before she tapped the the Pokeball with her beak.

 **Music: I Caught A Pokemon - Pokemon Anime**

"I caught a Pidgeotto!" Sonic shouted, posing dramatically. Latias clapped, knowing Sonic made the right choice. Shaymin, on the other hand, was sleeping in her Land forme, after finding a comfortable spot on Latias's back. A smile was on her face, and flowers bloomed all over her back.

* * *

 **Yo, have you seen Nintendo's Final Announcment? Cloud, Corrin, and Bayonetta confirmed for Smash!**

 _ **Sonic's Team:  
(If you are curious, then here is their personalities)**_

 _ **Shaymin F (Quite energetic and curious about it's surroundings. She's got a short attention span, and when nothing's happening, she looks for a comfortable place to sleep.)  
Latias F (Can't bring herself to hurt a fly. She's very cautious, and will heal anybody in need. She made friends with almost every legendary.)  
Pidgeotto F (While she prides on her power and will never back down from a challenge, she's a bit sensitive for her friends.)**_

 _ **(PS. Yes I know all of Sonic's Pokemon are currently females. I did this for a reason.)**_


	3. Chapter 2: Eggman and Shadow Pokemon!

**Sorry for the late update, I was all caught up in holidays, games, food, and family. Here is the next chapter! It's pretty important. Hope you like it.**

"Speech"  
" _Pokemon Speech"  
Thoughts  
_ _Pokemon Move_

* * *

 **Previously...**

* * *

 _"Land ho!"_

 _ **"Pidgeotto: The Bird Pokemon. Pidgeotto is the evolved form of the Pidgey."**_

 _"You looking for a fight, eh?" Sonic replied._

 _"I caught a Pidgeotto!" Sonic shouted, posing dramatically._

* * *

 **Chapter 2: Eggman Strikes! Shadow Pokemon!**

* * *

Sonic and friends made their way to Cherrygrove city and noticed that everything was in chaos! Three giant birds were thrashing about and wild Pokemon were scurrying to and fro. Two young boys were trying to calm the yellow bird down, and a girl was playing support in case a Pokemon got hurt. A young adult was fighting the orange and blue birds.

"What is going on here?!" Sonic whispered to Latias and a recently woken up Shaymin.

" _That's the legendary bird trio, Articuno, Zapdos, and Moltres. But why are they here causing all this chaos?_ " Latias replied. Sonic was about to charge in when another adult flew in with a big white bird with a blue belly to stop the fighting.

"Long time no see Gary! Did you get my notes on the discovery of new creatures?" The trainer asked. _Why does he look familiar?_ Latias wondered.

"This isn't the time for that Ash... At least you brought Lugia with you. It should be able to calm down the birds." The man named Gary said. Latias' eyes widened at the name, even if she was invisible.

" _Friends! Why do you cause so much chaos? I'm here to bring you peace!_ " Lugia telepathed.

"I wonder why they were so agitated?" Gary wondered out loud.

"This is not some natural disaster. Somebody must be behind all this." Theorized Ash. A fat person with black pants and a red jacket came flying over in a mechanical hovercraft.

"Lugia! You are so majestic in person!" He exclaimed. Sonic lightly gasped.

(Music: Chaotic Calamity That's One with a God - Tales of Zestiria)

"That's Doctor Eggman!" Sonic whispered.

" _You know this guy?_ " Shaymin asked.

"He is the big villain in my world. He's always causing mischief, and I'm always there to stop him. In fact, he's the reason why I'm here in the first place."

"Who is this guy?" Gary asked.

" _I do not know this person, but he holds great anger and evil inside of him._ " Lugia warned.

"I am Doctor Eggman! The greatest scientist in the world!" He shouted. "But a man as great as me does not get everything I so utterly deserve. But I shall rule this world! And anybody that tries to get in my way will be stomped!"

"Shut it old man! What do you want?" Gary growled.

"The answer is simple. I want Lugia! If I were to control this world, I'm going to need some help!"

"So that settles it. You caused the birds to go on this rampage so that Lugia would have to appear to calm them." Ash frowned.

"Right answer! And now, I shall take my prize!" Eggman threw a black and purple Pokeball. Lugia was captured. Everybody gasped, as a claw picked up the ball. Sonic jumped out from the hiding place.

"Hey Eggman! What have you done to Lugia!?" Sonic yelled. Latias and Shaymin followed after.

"Ahh, Sonic! Welcome. What you have just seen is the beginning of my reign!" He held up the ball now containing Lugia. "With these Dark Balls, I shall become invincible! And you won't be able to stop me!" He opened the Dark Ball. Lugia had a dark aura around him, and his eyes were red. "Shadow Lugia! Take me to Violet City!"

" **Yes, Master.** " He spoke in a deep, monotone voice, as they teleported away.

(Music: Cherrygrove City - Pokemon HGSS)

"Who... What are you?" Asked Ash, seemingly unfazed by the event that just unfolded.

"My name is Sonic! Sonic the Hedgehog."

" _Ash... Is that really you?_ " Latias telepathed.

"Do I know... Wait, are you the same one from Altomare?" Latias smiled, and hugged Ash.

" _You remember me!_ " Latias laughed. "Nice to see you too." Ash patted her head.

"That Eggman guy seemed to know who you are. Do you know him, Sonic?"

"Yes. He is an evil mastermind from my world. My friends and I constantly stop his evil plans. But one time we failed. He tried to send me to another world, but something went wrong and now we are here, and he came with us. Now he has Lugia... He mentioned going to Violet City, right? Where is that?"

"Just follow the path north of this town." Ash told.

"Got it. Latias, Shaymin! We've got a villain to catch!" Sonic told, returning said Pokemon to their Pokeballs and _boosted_ off.

"Wow, I guess he isn't called Sonic for nothing." Gold commented. (In case you didn't know, Gold and Silver were fighting off Zapdos)

* * *

Sonic hit the brakes pretty quickly when he saw the gate to Violet City blocked off. Some guard was blocking the way, and a guy in all blue was complaining.

"What do you mean I can't enter Violet City!? I'm the gym leader!"

"I was given strict orders to not let anybody in." The guard said in a deep voice that clearly meant he didn't like anything in the world. _Screw that, I'm going over!_ Sonic thought. He sped off towards the wall, and climbed up it and jumped down from the other side. Hearing noises from the big, old tower, he headed over there immediately. There were Bellsprouts everywhere, even one big Victreebel. However, they were all Shadow, just like the Lugia.

 _I'm going to get you Eggman._ Sonic thought. A man came rushing over in panic. "Please, you have to help us! This man came in with a weird Lugia and now every Pokemon is going crazy! There is even a giant Victreebel!"

"Hold on old man, I'll help calm them down!" Sonic released Latias, Shaymin, and Pidgeotto. "Girls, we've got a big fight ahead of us!"

 **Boss Battle: Shadow Victreebel**

(Music: Battle Mode Theme 2 - Pokemon XD: Gales of Darkness)

The Victreebel hopped over and shot many _Razor Leaves_ , but nobody was harmed. Latias shot _Mist Balls_ and Shaymin used _Magical Leaves_ from afar, while Pidgeotto got in close and started _pecking _ it. She dodged a few _Vine Whips,_ but eventually got hit and flinched from the power. During that time, Victreebel summoned a _Leaf Blade_ and sent her flying to the wall with an audible thud.

" _Pidgeotto_!" Latias cried out. In the moment, she didn't notice a _Leaf Storm_ being charged up, and got launched into the wall, fainting. Many Shadow Bellsprouts came over, and Shaymin tried to take them out but there were too many. Overwhelmed by _Razor Leaves_ , she failed to prepare for a _Leaf Storm_ and fainted as well. Pidgeotto was back, sending strong _gusts_ of wind toward the Bellsprout. They were blown back into the wall and fainted. But Victreebel came out from behind stuck down with a _Leaf Blade_ , making her faint.

 _Why is it so strong?_ Sonic thought. "Fine, I guess it's my turn now!" Sonic _spindashed_ into the Victreebel, dealing some damage. Bouncing back, he shot in a few _Homing Attacks,_ when the Victreebel _protected_ itself from his barrage. Letting go of the protection, it shot out a _Leaf Storm,_ only for Sonic to dodge and _boosted_ into the Victreebel, launching it into the wall.

(Music: Victory! Team Magma/Aqua - Pokemon Omega Ruby and Alpha Sapphire)

"Phew! I did it!" Sonic grinned. The Victreebel coughed something up before it fainted. "Whoa, that's a Chaos Emerald! No wonder why it was so strong." Sonic picked the green emerald up and put it in his bag. "Good thing we found it so soon." He returned his Pokemon to their balls and headed out for the Pokemon Center.

* * *

"Welcome to the Pokemon Center, how may I help you?" Nurse Joy asked.

"Can you heal up my Pokemon? We've got into a pretty rough fight with some of those Shadow Pokemon at the Bellsprout Tower." Sonic explained. Joy examined the damage for a few seconds. "Chansey, bring me the beds!" A faint _"Chansey!"_ echoed down the hallway. "Your Pokemon should be ready by tomorrow. How about you sleep in one of our guest rooms, Mr. Sonic? It's getting quite late."

"Sure. Thanks for helping us out."

"Your welcome."

* * *

 **That's a wrap! Some story, and our first boss battle! I'll be doing a team recap every time Sonic gets a new Pokemon, by the way.**


	4. Chapter 3: An Airborne Battle!

"Speech"  
" _Pokemon Speech_ "  
 _Thoughts  
_ _Pokemon Move_

* * *

 **Previously...**

* * *

 _"What is going on here?!"_

 _"That's Doctor Eggman!"_

 _"I want Lugia!"_

 _"Girls, we've got a big fight ahead of us!"_

* * *

 **Chapter 3: An Airborne Battle!**

* * *

Sunlight shone on Sonic's face through the open window, slowly waking him up. A new day has come, and our heroes were resting up after a big fight yesterday. Quite a few things happened that day. It worried Sonic, because Eggman has already enacted his plans to take over. Stretching, Sonic made his way out the door.

(Music: Route 201 - Pokemon Anime)

"Good morning Sonic! Your Pokemon are all healthy. Please, be careful out there. More and more Shadow Pokemon has started showing up recently." Nurse Joy told, handing Sonic a tray with his three Pokemon. "Would you like some breakfast before you go?"

Sonic searched through his bag for a moment. "Um, I don't have money."

"It's ok. We offer free services for trainers like you." Joy smiled.

"Really? Well, I'm in. I'm starving. I believe my Pokemon are hungry, too." Sonic threw out his Pokemon. Latias and Pidgeotto were wide awake, and Shaymin was still sleeping. "I believe we should snack up before heading out." Sonic told them. Shaymin's eyes blinked open at the word "snack." "I'll be right back." Nurse Joy walked to prepare some food.

" _How was that Victreebel?_ " Pidgeotto asked.

"I knocked him out good. I wish there was a way to turn them back to normal, though. But there was a reason he was quite strong." Sonic dug through his bag to pull out the green Chaos Emerald. Everybody gasped.

" _Pretty!_ " Shaymin's eyes sparkled. " _What is that?_ " Latias asked.

"This, is a Chaos Emerald. A jewel with the ultimate power. It can be used for things such as powering machines, but if the user is strong enough and well trained, they can use it to slow down time, warp to far places, or even achieve an ultimate form, in which the term is called, going super. This great power is what I fight to protect. If this falls into the wrong hands, then we're in big trouble. But I always end up using them myself to end evil. There are 7 Chaos Emeralds, and there will only be 7."

" _When did you first discover the Chaos Emeralds?_ " Latias asked.

"It was a long time ago... Wow, it really takes me back. Anyways, it was when Eggman first showed up, and I had to collect them all to restore peace. It was on my second adventure, when I first found my new best friend, that I found out that I can achieve a super form, and take down the biggest of monsters. And it was a few years later when I found out that the Emeralds could be used for more than just that, when I first met Shadow. We were rivals at that time, but when the entire planet was at risk, we teamed up and became friends to take down the threat."

" _What does the super form look like? Can you show us?_ " Shaymin bounced excitedly.

"Well, there's a problem. To achieve this super form, you must have all 7 Emeralds, and we only have 1." Shaymin deflated for a few seconds, then perked up again.

" _I think I smell food!_ "

"That must be our breakfast." Sonic commented as a Chansey and Nurse Joy came out with Pokemon food and pancakes. "Enjoy!" " _Here you go!_ "

 **A few minutes later...**

"Thanks for your service!" Sonic grinned. His Pokemon nodded. "Thanks! We hope you prevail!"

"Bye!" Sonic waved, as he headed out the door. This time, he decided to keep his Pokemon out. Violet City seemed a lot calmer now, and after looking at it, he noticed that it was quite purple. People were roaming around like nothing even happened. The same man in all blue from earlier came running up.

"Hey, your name's Sonic, right?" He asked. Sonic nodded. "Great! You're pretty famous around these parts, you know. Anyways, are you by chance trying to stop evil?" Another nod. "Then I think you should try the Gym Challenge."

"What's that?"

"There are 8 gyms in every region, and you have to challenge each gym leader. The gym leaders here test your strength against different typings, and make you test different strategies. Overall, it will help you grow stronger. After defeating all the gym leaders, you have to fight the elite four, then the champion to become the strongest trainer. Do you want to take it?"

"Sure, why not? Where is the first gym?"

"It's right here in Violet City! Right over there, the building with the brown roof."

"Thanks. Say, what's your name?"

"My name is Falkner."

"Ok, see you later." Sonic walked to the building. He tried to open it, but it wouldn't budge.

"Need help?" Said the same voice from earlier. "Huh? You know how to get in?" Falkner took out a key, and slid it into the key hole off to the side.

 **"Welcome Falkner. Unlocking...** **"** Said the mechanical voice. _Wow, the technology here is great!_ Sonic thought. Walking in, he saw the lights were off. Falkner flipped the lightswitch on.

"Do you know where the gym leader is?" Sonic asked. But Falkner just chuckled.

"You've been speaking to him all this time."

"What!?" Sonic jumped.

"Hey Jim-" Falkner shouted to a nearby person.

"It's Joe!" Joe cried.

"Whatever John. Can you be the referee this match?" Falkner called. Joe grumbled, and got to the referee stand.

"Poor Jack, everybody gets his name wrong." Sonic commented.

"It's Joe!" Falkner walked over to the other side of the room, and took out two Pokeballs.

"This will be a one on one match between Sonic and Falkner. No substitutions are allowed, but moves that involve switching out of the field can still be used. If necessary, the roof will be opened. This gym battle will be a test of how well you can take a constant barrage of high speed attacks. Now, bring out your first Pokemon!"

(Music: Undertale - Heartache (Orchestral Remix) - Hellkite Drake)

"Go Pidgeotto!" They both shouted. They landed with a sharp squawk.

"Ready? Fight!"

 **Boss Battle: Gym Leader Falkner accepts your challenge!**

The two Pidgeottos shot towards each other instantly before they could give a command, trying to send _pecks_ at eachother, but couldn't without taking a hit as well. They stopped a few seconds later, then tried to send _g usts_ of wind. Soon, Falkner's Pidgeotto went in for a _quick attack_ and hit Sonic's Pidgeotto, but instantly recovered and started _pecking_ her opponent. He flew back and went for a _quick attack_ , but Sonic's Pidgeotto dodged. They both went full speed ahead with _quick attacks_ to the point where you couldn't tell what was happening. Soon, they both fell down, fainted.

"Both Sonic's and Falkner's Pidgeottos are down. Please send out your next Pokemon." Said Joe. Falkner returned his Pidgeotto.

"Ready for this Shaymin?" " _I sure am!_ " Said Shaymin, who took the time to change into her Sky Forme.

"Go, Pidgeot!" Falkner shouted. "Let me show you the true power of bird Pokemon!"

(Music: Pokemon Black and White - Decisive Battle / Last Pokemon Music (Orchestrated ) - YoshiDude12)

"Sonic sends out his Shaymin, and Falkner sends out Pidgeot. Next Pokemon that goes down loses. Next round, begin!"

"Pidgeot, _Agility_!"

"Shaymin, _Leech Seed_! Keep draining it's health! Go in for some _Quick Attacks_!" However, Pidgeot dodged the quick attacks with a huge boost of speed.

"Whoa, that's fast!"

" _You are one to talk, Mr. Fastest Thing Alive._ " Latias telepathed. Sonic sweatdropped.

"Use _Growth_!" Shaymin relaxed and felt stronger.

"Pidgeot use Twister!" Pidgeot flapped her wings quite hard, and a very strong _Twister_ formed, pulling in Shaymin. "Shaymin! Stay strong! Try using your _magical leaves_!" Shaymin couldn't see anything inside the twister, and the howling winds blocked out noises. " _He said to use_ Magical Leaf. _"_ Latias telepathed. Shaymin looked in a random direction. Using a _Magical Leaf_ as a guide, she found Pidgeot's movements and sent a barrage of _Magical Leaves,_ doing quite some damage. But she kept one to keep track of movements. Suddenly, Pidgeot burst through to _Wing Attack_ at nothing, seeing how Shaymin flew above. She then sent a final barrage of _Magical Leaves._

After the twister died down, they found a heavily panting Shaymin on top of a fainted Pidgeot.

"Falkner's final Pokemon fainted! Sonic is the winner!"

(Music: Victory! Gym Leader - Pokemon ORAS)

"Shaymin! You did it!" Shaymin flew over towards Sonic and gave a hug and giggled. Dropping her invisibility, Latias telepathed, " _Here, have a Heal Pulse._ " She also healed up Pidgeotto. Falkner walked over with a smile.

"You have impressive flying types. I hope you proceed and prosper with power. And as proof as victory, here is your Zephyr Badge."

"All right! We got the Zephyr Badge!" Sonic posed dramatically as Pidgeotto and Shaymin hopped into the air. Latias shrugged, and followed along.


	5. Chapter 4: Vs Lugia!

"Speech"  
" _Pokemon Speech_ "  
 _Thoughts  
_ _Pokemon Move_

* * *

 **Previously...**

* * *

 _"My name is Falkner."_

 _"This will be a one on one match between Sonic and Falkner."_

* * *

 **Chapter 4: Vs. Lugia!**

* * *

 _A few hours later..._

(Music: Route 201 - Pokemon Anime)

Sonic was fairly acquainted with the Violet City. The citizens knew Sonic wasn't a Pokemon, and treated him like any other human. He bought some medicine from the Pokemart, as well as some food for when they leave soon. He let his Pokemon roam the city and the nearby outskirts.

Sonic was sitting down on a bench when a familiar man walked over. "Hey! Nice to meet you again, Sonic." Sonic took a moment to swallow the bite of his Chili Dog.

"You said your name was Ash, right?"

"Yeah. We heard about how you helped the monk in Sprout Tower, and your skills in battle. I'm very impressed! You remind me of myself." Ash praised, as Gary walked over.

"Alright alright... that's enough of that. We need to find this elder and I'm willing to bet this strange man he was talking about is none other than Eggman."

"Elder Li should know how to purify these unnatural Shadow Pokemon." Said a passerby from Sprout Tower. Sonic managed to hold his laughter from the irony of Li's name. Three more people came over, which was the same group fighting off Zapdos earlier.

"Well well well! So the gang is all here as expected!" boomed a voice.

(Music: Chaotic Calamity That's One with a God - Tales of Zestiria)

"Eggman!" Everybody shouted.

"What do you want?" Sonic asked, getting ready for a fight. Three certain Pokemon flew in front of Sonic, each with the same expression.

" _What are_ YOU _doing here?_ " Latias angrily telepathed. But Eggman just chuckled, which grew into a short laughing fit.

"Oh ho ho! What sort of heroic adventures are you up to? You aren't trying to stop me or anything silly like that, right?" Ash just growled.

"Silly? Not only are you kidnapping innocent people, but you are also turning innocent regular Pokemon into shadow."

Eggman sighed. "You just don't get it. This world is not a place of fairness, people like you, people who do good... often pay. So I say, why be good at all? We all must pay! We shall all live in the shadows!" Eggman shouted.

"The _only_ person that will pay is you, Eggman! And your shadow will be that of the jail cell!" Ash called out.

"Sure! I'll pay after you defeat my friend here!" He threw a Dark Ball, yet it didn't hold Lugia. It instead held a strange, grey, biped Pokemon with a green tail.

"Th-thats Mewthree!" Gary gasped. Silver, Gold, Sonic, and his Pokemon looked confused. They sure did know about a Mewtwo, but certainly not Mewthree.

"Yes, I did find your friend with the unoriginal name. To make things fair, I'm going to make sure your friends don't interfere with our match. They get to wait with the others. Mewthree! Shadow Capture!"

" **Yes, master.** " He spoke in a monotone voice, just like Shadow Lugia did. Raising a hand, he snapped his fingers, and a circle formed around the group. A moment later, they were gone. All but Ash.

* * *

(Music: But Nobody Came - Undertale)

There was no darkness, yet all you could see was black. There was nothing, yet you could see people.

"Where are we? Is this where Mewthree took Lugia?" Latias spoke. Then realized that her voice was a little different.

" **SHUT UP, YOU BIG WIMP!** " The girl from earlier shouted. They realized they never got her name.

"Wait, they can understand us?" Pidgeotto asked to nobody.

" **GET OFF MY MOUNTAIN!** " Shouted a hiker.

" **I HATE POKEMARTS!** " Screamed a teenaged girl.

"Everybody seems mad in here..." Shaymin frowned.

" **SHUT UP SHAYMIN!** " Silver yelled. The Gratitude Pokemon flinched.

" **NO YOU SHUT UP!** " Roared Gary.

" **WHY DON'T BOTH OF YOU SHUT UP!?** " Screeched Gold.

"Huh, its just a hunch, but it appears that this place only affects humans." Theorized Sonic.

"That would make sense. Hey, look! It's Lugia!" Latias pointed.

"Wait, I thought you were captured in that Dark Ball?" Shaymin wondered out loud.

"It appears that this Dark Ball doesn't seem to be made for holding humans, so that's why they are acting right now. But this is the Dark Ball we are inside, and it makes us all connected. But because its main guest is me, it will break if I take enough damage. You must fight me if you want to live! If you do enough damage, it will cause a flux in this realm and will release you."

"B-but, what will happen to you, Lugia?" Pidgeotto inquired. Lugia hesitated.

"...I can not escape from this place. ...I'm conscious inside here, but when I'm out of the ball, I can no longer take control of my actions. And the longer I'm in here, the more corrupted I become. Soon I will become a full Shadow Pokemon, just like the others you've seen. In the future, I may be forced to fight you. ...You have to break free of this cage. You have to save me- no. You have to save the world."

After a few seconds, Sonic nodded. "If we have to... then there is no other choice."

(Music: Hopes and Dreams / Save the World - Undertale Orchestral Rock Remix - CabbitSD)

 **Boss Battle: Lugia**

Shaymin, who couldn't seem to get into her Sky Forme due to the properties of the Dark Ball, started to use _growth._ Pidgeotto, who was training with Falkner earlier, whipped up a _Twister_ , and Latias shot a _Mist Ball. _ Sonic hit Lugia with a _Homing Attack_. Lugia flapped his wings and sent out a strong _Gust_ towards Shaymin, but Latias picked her up with _Psychic_. Lugia went for a _Rain Dance_ , followed up by a _Hydro Pump_. The rain increased the damage done, dealing high damage to Latias, and slight damage to Shaymin, who was sitting on Latias.

After recovering, Shaymin shot a volley of _Magical Leaves_ after using _growth_ some more, dealing a bit more damage than usual. Looked like a critical hit. Latias kept flying around to distract Lugia, while Shaymin still riding Latias' back kept using _growth_ and _Magical Leaf_. Lugia charged up an _Aeroblast_ , but Sonic round-house kicked Lugia in the back of his head, causing him to aim too low. They all took the chance to _tackle_ as hard as they could.

With a sharp cry, everything started to become distorted. "Good job, everybody." Lugia managed to say before a bright flash shot out.

* * *

(No music)

"Hey, wake up!" A distance voice cried. Groaning, Sonic got up. "Ugh, my head hurts..." They seemed to appear right where they last left off, except the sun was much lower. To Sonic's dismay, his unfinished Chili Dog wasn't there anymore. Everybody slowly got back up. "You're back!" Ash said. "What happened?"

"Well, it's a long story..."

* * *

Sonic and friends visited the Violet City Pokemon Center to rest for the night. Handing his Pokemon to Nurse Joy, he layed down on the bed and quickly fell asleep.

* * *

 **The Next Day...**

* * *

(Music: Clock Town Day 1 - LoZ Majora's Mask Reorchestrated - Zelda Reorchestration (ZREO) )

Sonic yawned as a brand new day awakened. He let his Pokemon out for breakfast.

" _I'm still kind of worried about Lugia._ " Shaymin drooped.

"You did the only thing you could. There was no way you could save Lugia." The girl comforted. She said her name was Zai.

After breakfast, they packed up and decided to leave Violet City. It was a foggy morning, and the sky was still a brilliant yellow. As they were heading out, however, they were stopped by Ash.

"Hey Sonic, I was looking for you."

"Hmm? What do you need?"

"I was given a request by Professor Oak, he wanted me to find you and tell you to come visit him. He has something for you."

"Sweet! Where can I find him?"

"He has a house in the route between this city and Cherrygrove City, so right over there."

"Thanks!" Sonic sped off towards the house. There was only one house on that route, so it must be his house. He reached a house, and the sign in front confirmed it was Professor Oak's. Knocking on the door, a faint "Coming!" echoed through. A few seconds later, the door opened.

(Music: Professor Oak's Lab - Pokemon Red, Blue and Yellow Orchestrated)

"Ah! You must be the Sonic I've heard of. Come right in." They walked over to a table and Sonic sat down.

"So what did you need me for?"

"I've heard of you from Ash and Gary. You sound like quite the world savor, much like Ash was back in the day. You may have two legendaries already, but you still don't have a full team. I have a bunch of Eevee as pets, and I'm sure some of them would quite like the adventure. Would you like one?"

"Well, what is an Eevee?"

"Oh ho, silly me, giving you something you don't have a clue on. Here, how about you scan one with your Pokedex?" Prof. Oak took a Pokeball and opened it. Out came a fluffy, brown, cat-like Pokemon. Sonic took out the Pokedex and scanned it. It seemed quite surprised at seeing Shaymin and Latias.

 **"** **Eevee, the Evolution Pokémon. Eevee is a unique Pokémon that can adapt to its environment by changing its form and abilities when evolving. It has a total of eight different evolutions."**

"I think I will take one." Sonic dug through his bag and pulled a Pokeball out. "Hey, do you want to come with us?" The Eevee thought for a second then pushed the button on the ball.

"Take good care of him, won't you?"

"I will. Thanks, Professor Oak!"

* * *

 **Sonic getting an Eevee was inspired by Pokemon Insurgence, a great fan game. Expect more things from there. Cookies to you if you find out which Pokemon fan game this story is partially based on. If you couldn't tell, I am basing Sonic's team off of good Pokemon that can go fast. New Pokemon! And finally, something huge is coming up... be warned.**

 _ **Sonic's Team**_

 ** _Shaymin F (Naive)  
Latias F (Calm)  
Pidgeotto F (Adamant)  
Eevee M (Quirky)_**


	6. Chapter 5: Twisted Shadows

"Speech"  
" _Pokemon Speech_ "  
 _Thoughts  
_ _Pokemon Move_

* * *

 _ **Previously...**_

* * *

 _" **Yes, master.** "_

 _"If we have to... then there is no other choice."_

 _"Hey, look! It's Lugia!"_

 _"Well, what is an Eevee?"_

* * *

 ** _Chapter 5: Twisted Shadows_**

* * *

(Music: Route 201 - Pokemon Anime)

Sonic and his Pokemon made their way down the only Route they could, which was Route 32. One side seems to be blocked off, so they went to the Ruins of Alph nearby.

" _So, you're all female, right?_ " Sonic's new Eevee asked. They nodded in confirmation. He just sniggered, however. " _I get it! You must be travelling with Sonic because you must have a crush on him!_ "

" _What-_ "  
" _Whoa-_ "  
" _Huh?_ " The girls stammered. Shaymin just looked confused on what that term meant.  
"What? No, that's clearly not it. There's no way, right?" Sonic asked. The girls, however, just blushed.

" _Wait you can understand Pokemon?_ " Eevee asked.

"Well I'm not a human."

" _Touche._ " They decided to go inside the Ruins of Alph.

(Music: Pokemon GSC/HGSS Dark Cave Remake - OcarinaSchief)

There were a bunch of letter-like Pokemon floating around. He pulled out his Pokedex.

 **"Unown, the Symbol Pokémon. Unown are said to have existed since ancient times. There are many in form and shape but little is known about this mysterious Pokémon. They can use telepathy to communicate to eachother."**

Like the Pokedex said, they all seemed to have one circle in the middle, which held the eye. Upon further inspection, they all looked like letters, an exclamation mark, or a question mark. There seemed completely empty, excluding a wall and a bunch of stones. " _These seem interesting..._ " Latias noted. She went to inspect them, but the Unown started to go crazy and attack! "Whoa!" The Unown tried to take away the strange stones, but Sonic charged up a _Lightspeed Attack_ and charged at all the Unown.

" _Wow, that was very, fast._ "

"You'll get used to it. But those stones must be important." Sonic smirked. All the Unown fainted, and the room was silent. They took a closer look at the stones. It had a bunch of letters on it. "Hmm... I wonder what these would say when all arranged up. I wish my friend was here. He'd be able to decode this."

" _Well, we'll be able to see him when you return home._ " Eevee said. The girls looked a bit down at that sentence. Eevee sniggered. " _Shut up!_ " Shouted Pidgeotto.

"Well, nothing here seems important. Maybe the other cave has something." His Pokemon agreed. On the way, they met with Ash and Gary.

"Why are we even here? I've researched this place plenty of times... the message on the walls have nothing to do with Shadow Pokemon... Waste of time..." Gary complained.

"Hey Ash! Where is Zai and Silver?"  
"Oh, Zai stayed with Silver, he wasn't feeling good. Did you find anything interesting? Check again to make sure."

However, the sight they saw upon entering was horrifying.

" _What the!?_ " Latias shouted.

"They are all Shadow!" Sonic grunted. "The nerve of that Eggman..." A big Pokemon jumped down from the ceiling. " _No way-_ "

(Music: Chaotic Calamity That's One With a God - Tales of Zestiria)

" _Is that-_ "  
" _Entei!?_ "

"I guess this is another Legendary Pokemon... Another one has already been took down, huh?" Sonic frowned. Shadow Entei roared, as a figure jumped off it's back.

" **We have reached our destination. And the target is right here.** " Said a familiar voice.

"Shadow!?" Sonic shouted.

" _You know this guy?_ " Eevee asked.

"He's one of my friends. He's a bit grumpy, but quite powerful. Turns out that he can be turned into Shadow as well... Heh, I just realized the irony of that." Sonic tried to joke.

" _This isn't the time for that, Sonic. It's time to fight!_ " Latias prepared.

 **Boss: Shadow Entei and Shadow** **Shadow**

(Music: Power of "NEO" - IKARUS Remix) (Undertale music is great, okay?)

Shadow Shadow began with a _Homing Attack_ at Sonic, which he dodged. Sonic ran outside, for more space to battle. Entei began by using _Mean Look_ on Shaymin, stopping her in place. He then threw a _Lava Plume_ at her, but Latias took the hit. She took a bit more damage than she thought she would, but healed herself with a _Wish_. Shaymin and Eevee noticed that the Shadow Unown were going towards the strange rocks, so they covered them.

Pidgeotto charged in with a _Wing Attack_ , then set up the _Twister_. Entei used _Extrasensory_ to get rid of the attack, and fired a _Flamethrower_ at Pidgeotto. She got burnt pretty badly. After Latias' _Wish_ healed her, she used _Heal Pulse_ on Pidgeotto to keep her fighting. She began setting up a _R_ _eflect_ and _Light Screen_ to weaken the attacks received. With Latias' support, they quickly took down the Unowns, and they all ganged up on Entei.

* * *

Sonic ran through the trees, dodging and weaving around the area while trying to attack Shadow. Any attacks they threw were dodged, until Sonic figured out a pattern. After Shadow used a _Homing Attack_ , he seemed to slow down for a moment. Sonic quickly took the chance to kick him full force. He went flying into the trees, but quickly got back up. The battle turned into a fist fight from there, and a few hits were occasionally took. A few trees were knocked down, and any wild Pokemon knocked out quickly ran from the scene. One of Sonic's kicks sent Shadow into a tree, and Sonic immediately _Homing Attacked_ him, knocking him unconscious. He seemed to disappear from reality.

"A fake Shadow... Who could be behind this?" Sonic wondered, then went to check on the others.

* * *

Shadow Entei was taking a lot more damage, but soon realized that Latias was healing the others. It used _Eruption_ on everything around it, but it was more focused on Latias, then immediately bit into her with a _Fire Fang,_ knocking her unconscious. Throwing her aside, it was about to charge another _Eruption_ , but was knocked to the wall by Sonic's _Homing Attack_ _._ It was then knocked unconscious by his _Stomp,_ and faded out of reality.

(Music: Victory! Champion - Pokemon ORAS)

"The Entei was fake... Just like the Shadow I fought. Who could be behind this? But, we defeated them! Let's rest up, shall we?" Sonic cheered. A burnt Shaymin, a singed Pidgeotto, and a scorched Eevee all agreed.

(Music: Route 201 - Pokemon Anime)

They returned to the top, and started to heal up. "What happened? And why does it smell like a barbecue?" Ash asked.

"We were attacked by a Shadow Entei! There was also a Shadow version of my friend, also named Shadow, but they seemed to disappear after fainting..."

"A Shadow Entei!? Wait! Now that I think of it, this has happened to me before! The Unown can make fake Pokemon if somebody truly wishes for it... Do you think Eggman made the wish? Grr, what is he trying to do? I'm going to go in and investigate. Meet me in there is you wish, I'm going to talk to Gary." The two made their way down the ruins.

Sonic unpacked, and took out healing items to restore everybody's health. Sonic put out the burning on Shaymin, of which Latias could not have fixed if she were conscious, and healed the others. Latias returned to her Pokeball, because it would be a bit before she woke up. " _It's about 1:00. We should have lunch._ " Shaymin told after checking the position of the sun. Sonic's stomach rumbled.

"Well I can't say no." He agreed.

* * *

 **1**


	7. Chapter 6: The Time Travellers

**Edit: Ho-Oh now stays for a little bit, and helps train the team. But specifically Quilava.**

"Speech"  
" _Pokemon Speech_ "  
 _Thoughts  
_ _Pokemon Move_

* * *

 _ **Previously...**_

* * *

 _"They are all Shadow!"_

 _"_ It's time to fight! _"_

 _"Who could be behind this?"_

* * *

 ** _Chapter 6: The Time Travellers_**

* * *

(Music: Route 201 - Pokemon Anime)

"All these writings are completely different from last time I was down here. Which makes no sense, because this place is thousands of years old... The Unown seem to be trying to take the chunks of writing from the walls. Are they trying to get rid of them or protect them? Hard to tell..." Gary said. "Hmm, I did manage to find one intact word, and it says Celebi..."

 _The ruins have changed since we last came here... but how is that possible?_ Wondered Ash.

* * *

After Latias recovered, they decided to visit Ash once more. "Gary says the words have changed since last time he came here. Oh hey, listen. I appreciate everything you've done. You are a great trainer and I hope we can battle one day, but I think it's time to part ways. Don't worry about us, we have stopped many bad guys, and even really strong Pokemon. Just go out there and have fun! You should go East of Route 32, then go South. Good luck, and I hope to see you again."

"Okay, thanks Ash. Well, see you later." Sonic replied.

"Good luck!" Gary called. As they reached the surface, they did notice that the path wasn't blocked anymore, and they headed on. Many wild Pokemon played in the grass, and the sight warmed their hearts. " _Wow, this is a nice place._ " Shaymin commented. They headed down the path.

* * *

 _Meanwhile, at the Ruins of Alph..._

* * *

"Hmm... Where did the Unown go?" Ash wondered.

(Music: Chaotic Calamity That's One With A God - Tales of Zestiria)

"This... This can't be! ASH LISTEN TO THIS!" Gary shouted.

"DID YOU FIGURE IT OUT? WHAT DOES IT SAY!?" Ash replied.

"I've arranged the words in every way possible, but this is the only one that makes sense. It says, 'Safe with Celebi save Silver fix everything hide Mewthree coming.' That's all. The same words are repeated over and over again. I've done some testing, and these marks date back 10 years ago. Yet I'm positive these weren't here last time. The fact that it mentions Celebi must mean that somebody must have traveled back to the past, around 10 years ago, to send us this message."

"Message? It sounds more like a warning! 'Hide Mewthree coming.' I've got a bad feeling about these words..."

* * *

 _A few minutes earlier..._

* * *

"That Shadow Entei should keep those idiots away for a time. Mewthree, how much more until Shadow Lugia is complete?" Asked Eggman.

" **Not even close, Master... Allow me to absorb more people into the Shadow Realm and Lugia will be ready in no time, Master...** "

"HOW MANY TIMES DO I HAVE TO TELL YOU! If you absorb too many, you will lose control!"

" **Master, I must correct you...** "  
"What are you talking about?"  
" **You said I will lose control when in reality it is YOU who will lose control... don't forget master... I'm Psychic. I can read your MIND!** "

"Grrrr! How dare you defy me!? Return to your Pokeball, NOW!" He shouted.

" **I choose not to obey you, instead I will use Shadow Capture... on YOU!** "

"What!? No! Stop! I have an Earth Badge! You MUST obey me!" He yelled, trying to run away. But Mewthree laughed maniacally, as Eggman was Shadow Captured.

" **That fool, nobody can escape my Shadow Capture... Now to capture all the other fools that live in Johto! If only I can be everywhere at once... Hmm, I think I can...** " Mewthree used a move that was much like Double Team, yet very different.

" _ **SHADOW TEAM!**_ **Nobody will be able to stop us! Go! Go and absorb every living thing you see!** "

* * *

 _Back with Sonic and Co..._

* * *

(Music: Route 201 - Pokemon Anime)

"Hey! Wait up for us!" Shouted Zai. She, Silver, and Gold came running up to Sonic. "You didn't think that we would leave you all alone out there, did ya Bunny?" She said.

"I think the term would be, Hedgy." Gold joked.

"Well, I thought I was feeling better, but Gold ruined it..." Silver complained.

(Music: Chaotic Calamity That's One With A God - Tales of Zestiria)

A fisherman from around the corner screamed. "AHHH! NOT MY FISH!"

"What just happened? Is that... Oh no!" Zai screamed.

"Whoa!" Shouted Gold.

"That's Shadow Mewthree! He just absorbed that Fisherman! But where is Eggman?" Wondered Silver.

"NO! STOP! I COMMAND YOU TO STOP!" Shouted a mysterious man.

"Wait, that's Giovanni! What's he doing here?"

" **You may be working with Eggman, but you shall belong where he is right now!** " Shouted Shadow Mewthree, absorbing him.

"That was my Grandpa!" Silver shouted, getting Mewthree's attention.

"AHHH! IT'S COMING THIS WAY!" Zai Shouted.

"Gold! Get out of the way!" Silver pushed Gold away, before he got captured with Zai and Silver. " **You belong inside... SHADOW CAPTURE!** " It shouted. " **ALL SHALL LIVE IN THE SHADOWS! Don't think I didn't see you, you are next!** " It shouted.

" _It doesn't matter who you are,_ " Started Latias, going visible.

" _But w_ _e are not going down without a fight!_ " Shaymin continued, going into her Sky Forme.

" _So if you are going to try and hurt our friend..._ " Pidgeotto snarled, starting to fly.

" _You will have to get through us, first!_ " Eevee finished.

Sonic kept away some tears. _I have great friends..._

"Don't leave me out!" Gold told, sending out his team, which consisted of a Quilava, a Shadow Pidgeotto, and a Shiny Spinarak. A big battle was ahead. They were filled with determination.

" **You FOOLS! You think you can stop ME!?** "

 **Boss Battle: Shadow Mewthree!**

(Music: Undertale Battle Against A True Hero Orchestra + Choir Arrange - Hellkite Drake)

Mewthree noticed that he was facing up against one of his own. " **You traitor... You shall be my target! Experience pain!** " Mewthree used a _Mean Look_ on the Shadow Pidgeotto, making him unable to move. " **Traitor?... I am a Traitor, but I am so for the greater good!** " Shadow Pidgeotto shouted. He blew up a _Twister_. All the other Pokemon went in for an attack, but it seemed barely harmed. " **Target! Bring pain to those around you!** " It shouted. A _Fire Spin_ appeared around Pidgeotto, and blew out in all directions, doing great damage, and fainting Pidgeotto. It's next target was Shaymin, and used another _Fire Spin_ before Shaymin could be healed by Latias. A few more went down as well.

" _This is not good. It keeps knocking them down before I can heal them!_ _It's completely breaking my barriers!_ " Latias telepathed.

"This is not good. Mewthree's too strong!" Sonic grunted.

"Are we able to do this?" Gold asked, worried.

Mewthree used _Psystrike_ to finish off the last Pokemon standing in his way. Now it was just an open pathway directly to Sonic and Gold. Gold fell to his knees, accepting his fate. Sonic, however, had other plans. Pulling out the green Chaos Emerald, he shouted, _"Chaos Spear!_ "

(Music: Spear of Justice Orchestral Remix - Malcolm Robinson Music)

Three green energy spears appeared around Sonic. Holding the Chaos Emerald in his left hand, he controlled the spears with his right hand. " **NGAHHH!** " He shouted, making the spears fly into Mewthree. It actually seemed like it was taking damage. Summoning as much as he needed, he threw some more, and made some more come out of the ground to block Mewthree. He fired a last barrage is spears into Mewthree, and it fainted. A few seconds later, it vanished from existence. Before they could celebrate, a green glow hung above Sonic, flashing.

"Whoa!"

The green flash died down to reveal two figures, a green pixie-like Pokemon and a white hedgehog. Somehow, this seemed to awaken all their fainted Pokemon.

" _Well done! But our fight isn't over, it has only just begun! Come, I have much to tell you!_ " Said the green pixie in a young voice.

(Music: Once Upon a Time Orchestral Cover - Penno Ink)

" _Urgh, what happened..._ " Spinarak groaned.

"Hi Sonic and Gold! Hi everybody! You all did well against that Mewthree clone." Said the white hedgehog.

" _Who are you?_ " Asked Shaymin.

"Well, my name is Silver. I can travel through time. I'm from Sonic's timeline, but from the future, and we never met due to some crazy events... Hard to explain. But hi!"

" _And my name is Celebi! I'm also a time traveller if you didn't know already. So, that clone you fought was much weaker than the original, but most would not have been able to resist as you did._ "

"You might be wondering where you are, but the better question is when."

" _We brought you back a few moments before Mewthree's attack. And to solve all this, we are going to have to travel to the past!_ " Celebi did a flip in the air.

"As we said, we have the ability to travel through time. We do our best to save the world, but sometimes we need a bit more firepower." Silver told.

" _It seems that all these events are linked to Silver's death, not the hedgehog, it's confusing with names. It's tied to the death of Giovanni's son, also named Silver. The only way to prevent this is to stop the 'accident' from happening._ "

"We have tried many times to stop the death, but it always failed. So this is why we came to you!"

" _Sonic, Gold, both of your families has a very special gift when it comes to saving the world. Gold's uncle was responsible for saving Kanto! With my help of course._ "

"Gold's dad, who is also named Gold, (you have a confusing family tree, don't name your child after yourself please.) was the best trainer in all of Johto! He even managed to beat Red in a full on battle!"

" _So now it is time for you to do something great!_ "

"Again, in Sonic's case." Silver commented. Celebi grunted. _I was trying to make an epic speech here..._ " _So come with us to the past! Will you do it? Will you come with us and save everything you hold dear?_ " Celebi smiled, almost like a demon. Everybody sweatdropped.

"Sheesh, you make it sound like we have a choice. So yeah." Gold confirmed.

"Well of course I would!" Sonic clenched his fist, with a smirk.

" _Hah! I knew you would! There is no time to lose!_ Let's GOOO!"

(Music: Once Upon A Time Orchestral - AkagitsuneYuki (music))

A green flash later, and they all appeared back at New Bark Town.

" _We made it intact! We are 10 years in the past! It looks the same, right?_ "

"Now here's what's happening. Both Gold's father and Silver have been invited to join the World Pokemon Tournament. It will take place later this year, and to get invited you must have 8 badges Your task is to get 8 badges and get an invitation. Sounds easy, right?"

" _Still with me? Good! Just make sure nobody finds out who you really are! This is very important! I have to go take care of a few things elsewhere, but I'll always be ready at Silver's call. Okay well get busy collecting those badges! Cheers!_ " Celebi left this time.

"You know, I kind of don't like Celebi." Silver admitted. A note appeared on his head, with the words,

"Dear Silver,

You too!

From, Celebi." Everybody sweatdropped.

" _You know, I'm thinking of something. I think I can..._ " Latias' form shifted, and in her place was a human with a simple white dress with bright red hair, with the two iconic tufts of hair sticking up. A necklace hung from her neck, with a blue triangle.

" _Well, I-I've always been interested in trying something like this..._ " Latias slightly blushed.

"Hey, that's pretty neat." Silver complemented, completely missing on Eevee and Spinarak's snickering.

* * *

(Music: Animal Crossing (Summer) - Mario Kart 8)

"Wow, this is a beautiful day." Sonic commented, walking along the first route. "The sun is shining, the flowers are blooming, and not a cloud in the sky..."

"It's a perfect day for a game of catch." Silver agreed. A flock of Pidgeys flew by, with a few Pidgeottos and two Pidgeots at the front.

" _I bet one of those Pidgeys is a baby me._ " Said Pidgeotto.

" ** _I bet my parents are around here!_** " Shadow Pidgeotto chirped in.

Latias seemed to notice something in the sky.

" _Sonic, look up there._ " Sonic followed Latias' finger and saw a majestic golden bird flying through the sky.

"Whoa... What is that?"

" _That is Ho-Oh, another Legendary Pokemon. She will appear before trainers with a pure heart. She might be trying to tell you something._ " Latias replied. True to her word, Ho-Oh peered down at the group, and gave audible wink, before flying off.

"...How do you make an audible wink?"

* * *

Later that night, when the crew were setting up camp on Route 32 and making dinner, Ho-Oh came for a visit. She seemed to have a bag.

" _Hello, Sonic. My name is Ho-Oh. I can tell that you are a great friend. Celebi told me about you. She told me about your mission. I do give hopes in that you succeed. I have a gift for you._ " Ho-Oh opened her bag, and pulled out a TM. " _This is a Technical Machine, a device that can instantly teach your Pokemon a move. This one contains my special move, Sacred Fire. Give it to your Pokemon as you please._ " Gold's Quilava perked up, but quickly went back to cooking dinner.

"Wow, this is neat! Thanks!" Sonic gave her a thumbs up.

" _However, I also come with a warning. I sense Shadow Pokemon in the vicinity, even though there should be none yet. Stay on guard. And finally, I have a quiz for you. If a Pokemon is caught in a Pokeball, what is one thing that can not be reversed?_ "

" _...Oh! I know! Can I answer!_ " Shaymin bounced after a moment, and Ho-Oh nodded. " _When a Pokemon is caught, and if_ _that Pokeball still holds that Pokemon, another Pokeball can't capture that Pokemon!_ " Shaymin smiled.

" _Exactly. A+. Sonic, I want you to capture me. Now not only will I be able to fly freely without the fear of another person catching me, but I can find you whenever I want._ " Ho-Oh pulled out another item from her bag. It was an orange and yellow Pokeball.

" _I plan on staying with you for a few days. Rough times are coming up, and you need to be prepared. I don't want any of you to get hurt._ " Ho-Oh blushed.

Spinarak and Eevee sniggered, writing another name on their sheet of paper.

Sonic took the ball in his hands, and caught Ho-Oh.

* * *

 **Gotta love me my Undertale references.**

 **A bit longer chapter, as you can tell by the word count. There will be a few moments that I will skip due to nothing happening in those moments.**

 **If you are curious, Ho-Oh's ball is a Fast Ball.**

 _ **Gold's Team**_

 ** _Quilava (F): Your average hero. She will protect those in need. She also likes cooking.  
Pidgeotto (M) (Shadow): Don't judge him by his dark aura. He's a pretty chill guy, and loves to have fun.  
Spinarak (M) (Shiny): A joker at heart. Loves pranks, and somehow gets around with unconventional and impossible ways._**

 ** _Silver's Team_**

 ** _Celebi (F): Has a short temper. Her New Year's Resolutions are to prevent less injuries, but she forgot which year that one was.  
Wow Silver, you better step up your game. Only one Pokemon so far, and she's not even here most of the time._**


	8. Chapter 7: Filling in the Gaps

**Chapter 7: Filling in the Gaps**

* * *

 _Please note that most of this chapter is filler. However, there is some important stuff. Not to mention I edited the previous chapter._

* * *

(Music: Route 201 - Pokemon Diamond/Pearl Remake Prediction)

"Hmm..." Sonic wondered.

" _What is it?_ " Latias asked.

"Would we have to re-challenge Falkner? It would be a bit suspicious if we had a gym badge from the future..."

"Yeah I can see what you mean. It's like somebody going on a quest then getting their primary goal at the beginning of the journey instead of the end." Silver said.

* * *

"Well that wasn't so bad." Sonic admitted ten minutes later.

" _If anything, they seemed weaker._ " Pidgeotto agreed.

" _Maybe we are just stronger._ " Quilava boasted.

"Well, in theory, if we are in the past, then it means that people would have less experience. But then again, we're 10 years in the past. There is no way Falkner's Pidgeotto would still be Pidgeotto after all that time." Silver told.

" _Maybe he gets new ones?_ " Latias theorized.

* * *

(Add in rain background noises)

The next day was a rainy one. It was hard for Quilava to train her fire-type attacks, especially her new Sacred Fire.

" _How would I even use it? Do I just breath a big fire ball?..._ " Quilava breathed heavily, and blew a _Sacred Fire_. Despite the rain weakening the attack, many chips of rock blew off of the wall.

" _Very good! And to use it so well on your first try._ " Ho-Oh complemented.

* * *

" _Now try the Sacred Fire as strong as you can._ " Entei told. He had the Flash Fire ability, so it wouldn't hurt him. Quilava blew her strongest one yet, and blew the _Sacred Fire_. Entei felt his power go up immensely, even with the rain. " _Wow, that is quite strong. I see you've mastered it. I believe your training is over. I hope we meet again._ " Entei bowed, then leaped away.

* * *

Just out of curiosity, Latias went invisible and headed back out to Altomare. It was just for a quick look. No harm in that, right? She was about to head back to Sonic when she was stopped by a disguised Latios.

" _Sister? I thought you were back at the garden?_ " Latios telepathed. Latias' eyes widened. It was then she remembered that Eon Dragons can sense others nearby. How could she had forgotten that?

" _What do you mean? I am back at the garden._ " A familiar voice replied. Latios blinked a few times before realization hit.

" _Wait a minute! If you aren't my sister... You must be an invader!_ " Latios growled. Latias forgotten how paranoid her brother was.

" _Wait! Stop!_ " Celebi's voice cried out. " _This is all just an accident. It's time travel problems. You see, this_ is _your sister, but from the future._ "

" _The future me? What is going on? Should I come over there?_ " Past-Latias' voice rang out.

" _No. We can handle this ourselves. Besides..._ " Latias trailed off just in case she said something she shouldn't say.

" _Something big will happen here soon. You need to stay._ " Celebi finished, and teleported herself and Latias away.

" _Now why on earth would you do that!?_ " She shouted.

* * *

(Music: Sans' Secret Room - Undertale)

"You know, I've been wondering..." Sonic started, still staring at the full moon. Eevee looked up at him.

" _Hmm? Go on._ "

"Eevees have many different forms. Which do you want to become?"

" _...Huh. I don't really know. I want to be something that can really help, but I don't know which one that is._ " Eevee stated.

" _You know, most of us is pretty fast. Maybe you should become a Jolteon. They are fast, too._ " Shaymin advised.

" _Well... Maybe. I don't know. If we are going into some big fights... then I want to help out as much as I can. Maybe Espeon? They can support and attack from far away._ " Eevee suggested.

"Whichever one is true to you, we shall find out soon." Sonic smiled.

* * *

Sonic couldn't sleep that night. He decided to take a flashlight and have a walk. It was still raining from the beginning of the day. Not that it bothered him. He felt the rain quite refreshing.

He found a frying pan on the ground. "I guess I'll use this as a drying pan." He joked to himself.

He soon stumbled across a pond in the woods. Taking a seat, he gazed upon the water, seeing the little ripples from the rain. He could barely make up the moon from behind the clouds. Suddenly, something _whooshed_ past him. Looking behind him, he saw nothing. But back in front of the pond, sat a beast similar to Entei, yet very different. This one was a light blue, with white spots on its belly and legs. A long purple mane was flowing behind it. Red eyes stared back at him.

" _You must be the Sonic I've heard about._ " She spoke. " _I am Suicune, Entei's sister. I now realize what makes you so popular around here._ " She stood up, and walked across the water, and circled Sonic. " _Yes, you are quite the interesting one._ "

"Well, hello Suicune." Sonic greeted. Suicune sat down next to him.

" _This pond is beautiful, is it not?_ "

"Yeah, it quite is." He agreed.

" _Sometimes I come to ponds around Johto and admire the beauty of them. Take my mind off of the past, and focus on the future._ _That is what we should all do, especially with a task as great as yours. Please, do take care. I do not want to see someone as great as you get hurt._ " Turns out that Suicune's blue fur does not hide a blush. " _I would love to stay with you._ "

"R-really?"

" _I do._ "

"Well, if you so want. All my stuff is back at camp in Route 32 though."

" _Then we shall make our way there._ " Suicune ran off quickily, with Sonic following up. Suicune had a _Tailwind_ to increase speed. When they got back to camp, everybody but Latias was sleeping.

" _There you are, Sonic. I was wondering where you went._ "

"Hello Latias." Sonic replied, searching through his bag and pulled out a Dive Ball. "I like fitting Pokeballs. I think this would look good for you."

" _Then I am ready._ "

"Welcome to the team, Suicune." Sonic tossed the ball, capturing the legendary beast.

Hidden from view was a Cresselia, who chuckled to herself. " _I knew she would go with him. She's been dreaming about him._ " She then flew away.

* * *

" _I quite enjoyed our time together._ " Ho-Oh told. " _But, I shall take my leave. I will still support you, however. I will let you know if anything pops up. If you want to see me myself, seek me in the Tin Tower. I will give you one last gift._ " She plucked one of her feathers from her wings. She started to fly off. " _Take care._ "

" _See you soon, Ho-Oh!_ " Suicune called.

* * *

" _Let me guess, Suicune is going with Sonic?_ " Entei asked Ho-Oh. A quick nod answered his question.

" _I'm worried for the girl. What will she do when Sonic returns to his world?_ " Raikou asked.

" _Suicune, along with all his other friends, will be heartbroken. I wish there was another way to change this..._ " Ho-Oh finished.

* * *

 **Quite a few legendaries seem to know about what is going on. Celebi shouldn't share secrets to a gossiper.**


	9. An Apology

**I am so terribly sorry. But I have reached a dilemma. I've been having serious writer's block. I have everything I need except the determination. Not to mention I'm making a fic based off of an unfinished game. The thought just came to me, and I've been wondering what would happen if I reach the end of it. Not to mention that this project is long, and writing it is tedious. I don't want to stop writing this fic, but at the same time, I do... I'm sorry for the ones that actually enjoyed this fic. But I can't continue on.**


End file.
